2D image to 3D in ImageJ or Fiji

[Josip Angelo Borovac]

Hello guys, I might have a stupid question but I am new to this.

I need to make a simple extrapolation of 2D image to 3D image and how would
this be (if at all) possible by using ImageJ (Fiji) or any of ImageJ
plugins?

What I have is a 2D sketches of image of mammalian retina (anterior/lateral
view) that contains different regions of neurons that are concentrated in
different regions (circled areas) and are drawn in different colors.
I want to clarify that this is just the model, so I do not have actual
data...i just need simple graphing conversion, no need for data
processing...this is just for simple presentation purposes.

It would be nice if I could get those 2D images in 3D view so I could
rotate it or make a simple animation where the retinal structure moves
around in circle.

I understand that I am asking more of the 3D modeling type of the problem
that could be solved potentially in applications such as Maya or 3DS Max
but I wondered if ImageJ has plugins of similar capabilities.

I'm new to this so please pardon for my level of knowledge, which is very
modest.


If you can help me with this that would be great. Thank you!



Josip A. Borovac
University of Split
School of Medicine

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[John Oreopoulos]

I'm sure others may know of a better way to do this, but something just to get you started. First put all your images into a stack using the Images->Stacks->Images to Stack command.
Next, take a look at the Image->Stacks->3D Project command documented here:

http://rsbweb.nih.gov/ij/docs/guide/146-28.html#sub:3D-Project...

Cheers,

John Oreopoulos



On 2012-09-19, at 12:18 PM, Josip Angelo Borovac wrote:

> Hello guys, I might have a stupid question but I am new to this.
>
> I need to make a simple extrapolation of 2D image to 3D image and how would
> this be (if at all) possible by using ImageJ (Fiji) or any of ImageJ
> plugins?
>
> What I have is a 2D sketches of image of mammalian retina (anterior/lateral
> view) that contains different regions of neurons that are concentrated in
> different regions (circled areas) and are drawn in different colors.
> I want to clarify that this is just the model, so I do not have actual
> data...i just need simple graphing conversion, no need for data
> processing...this is just for simple presentation purposes.
>
> It would be nice if I could get those 2D images in 3D view so I could
> rotate it or make a simple animation where the retinal structure moves
> around in circle.
>
> I understand that I am asking more of the 3D modeling type of the problem
> that could be solved potentially in applications such as Maya or 3DS Max
> but I wondered if ImageJ has plugins of similar capabilities.
>
> I'm new to this so please pardon for my level of knowledge, which is very
> modest.
>
>
> If you can help me with this that would be great. Thank you!
>
>
>
> Josip A. Borovac
> University of Split
> School of Medicine
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Joel Sheffield]

Hi Josip,

John has it right, assuming that your 2D images represent slices through
the eye at different distances.  One point, though, you may have to
manually enter the spacing between each of the slices in order to get a 3D
simulacrum.  You can do this simply once you establish the stack, by going
to Image>properties, and entering a Z spacing.  Also, you may have to
consider whether all of the images in your stack are in register with each
other.

Best of luck,

Joel


On Wed, Sep 19, 2012 at 12:52 PM, John Oreopoulos <
[hidden email]> wrote:

> I'm sure others may know of a better way to do this, but something just to
> get you started. First put all your images into a stack using the
> Images->Stacks->Images to Stack command.
> Next, take a look at the Image->Stacks->3D Project command documented here:
>
> http://rsbweb.nih.gov/ij/docs/guide/146-28.html#sub:3D-Project...
>
> Cheers,
>
> John Oreopoulos
>
>
>
> On 2012-09-19, at 12:18 PM, Josip Angelo Borovac wrote:
>
> > Hello guys, I might have a stupid question but I am new to this.
> >
> > I need to make a simple extrapolation of 2D image to 3D image and how
> would
> > this be (if at all) possible by using ImageJ (Fiji) or any of ImageJ
> > plugins?
> >
> > What I have is a 2D sketches of image of mammalian retina
> (anterior/lateral
> > view) that contains different regions of neurons that are concentrated in
> > different regions (circled areas) and are drawn in different colors.
> > I want to clarify that this is just the model, so I do not have actual
> > data...i just need simple graphing conversion, no need for data
> > processing...this is just for simple presentation purposes.
> >
> > It would be nice if I could get those 2D images in 3D view so I could
> > rotate it or make a simple animation where the retinal structure moves
> > around in circle.
> >
> > I understand that I am asking more of the 3D modeling type of the problem
> > that could be solved potentially in applications such as Maya or 3DS Max
> > but I wondered if ImageJ has plugins of similar capabilities.
> >
> > I'm new to this so please pardon for my level of knowledge, which is very
> > modest.
> >
> >
> > If you can help me with this that would be great. Thank you!
> >
> >
> >
> > Josip A. Borovac
> > University of Split
> > School of Medicine
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--


Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Josip Angelo Borovac]

Thank you very much Joel & John. It seems I am getting something with this,
I just need to tweak it a little bit and play more around it.

Best regards,

Josip

On Wed, Sep 19, 2012 at 8:31 PM, JOEL B. SHEFFIELD <[hidden email]> wrote:

> Hi Josip,
>
> John has it right, assuming that your 2D images represent slices through
> the eye at different distances.  One point, though, you may have to
> manually enter the spacing between each of the slices in order to get a 3D
> simulacrum.  You can do this simply once you establish the stack, by going
> to Image>properties, and entering a Z spacing.  Also, you may have to
> consider whether all of the images in your stack are in register with each
> other.
>
> Best of luck,
>
> Joel
>
>
> On Wed, Sep 19, 2012 at 12:52 PM, John Oreopoulos <
> [hidden email]> wrote:
>
> > I'm sure others may know of a better way to do this, but something just
> to
> > get you started. First put all your images into a stack using the
> > Images->Stacks->Images to Stack command.
> > Next, take a look at the Image->Stacks->3D Project command documented
> here:
> >
> > http://rsbweb.nih.gov/ij/docs/guide/146-28.html#sub:3D-Project...
> >
> > Cheers,
> >
> > John Oreopoulos
> >
> >
> >
> > On 2012-09-19, at 12:18 PM, Josip Angelo Borovac wrote:
> >
> > > Hello guys, I might have a stupid question but I am new to this.
> > >
> > > I need to make a simple extrapolation of 2D image to 3D image and how
> > would
> > > this be (if at all) possible by using ImageJ (Fiji) or any of ImageJ
> > > plugins?
> > >
> > > What I have is a 2D sketches of image of mammalian retina
> > (anterior/lateral
> > > view) that contains different regions of neurons that are concentrated
> in
> > > different regions (circled areas) and are drawn in different colors.
> > > I want to clarify that this is just the model, so I do not have actual
> > > data...i just need simple graphing conversion, no need for data
> > > processing...this is just for simple presentation purposes.
> > >
> > > It would be nice if I could get those 2D images in 3D view so I could
> > > rotate it or make a simple animation where the retinal structure moves
> > > around in circle.
> > >
> > > I understand that I am asking more of the 3D modeling type of the
> problem
> > > that could be solved potentially in applications such as Maya or 3DS
> Max
> > > but I wondered if ImageJ has plugins of similar capabilities.
> > >
> > > I'm new to this so please pardon for my level of knowledge, which is
> very
> > > modest.
> > >
> > >
> > > If you can help me with this that would be great. Thank you!
> > >
> > >
> > >
> > > Josip A. Borovac
> > > University of Split
> > > School of Medicine
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
> --
>
>
> Joel B. Sheffield, Ph.D
> Department of Biology
> Temple University
> Philadelphia, PA 19122
> Voice: 215 204 8839
> e-mail: [hidden email]
> URL:  http://astro.temple.edu/~jbs
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html